Starting phenix.real_space_refine on Mon Mar 11 04:42:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvv_32859/03_2024/7wvv_32859_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvv_32859/03_2024/7wvv_32859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvv_32859/03_2024/7wvv_32859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvv_32859/03_2024/7wvv_32859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvv_32859/03_2024/7wvv_32859_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvv_32859/03_2024/7wvv_32859_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 4528 2.51 5 N 1184 2.21 5 O 1255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 312": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7020 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2319 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 284} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1778 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2510 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 367 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 4.10, per 1000 atoms: 0.58 Number of scatterers: 7020 At special positions: 0 Unit cell: (112.86, 119.13, 85.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1255 8.00 N 1184 7.00 C 4528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.3 seconds 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 8 sheets defined 43.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'R' and resid 20 through 54 Proline residue: R 29 - end of helix removed outlier: 3.954A pdb=" N PHE R 53 " --> pdb=" O TRP R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 76 Processing helix chain 'R' and resid 78 through 87 removed outlier: 3.896A pdb=" N MET R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 128 Processing helix chain 'R' and resid 130 through 136 Processing helix chain 'R' and resid 139 through 162 Proline residue: R 149 - end of helix Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 181 through 184 No H-bonds generated for 'chain 'R' and resid 181 through 184' Processing helix chain 'R' and resid 187 through 209 Processing helix chain 'R' and resid 211 through 231 Processing helix chain 'R' and resid 238 through 266 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 268 through 273 Processing helix chain 'R' and resid 279 through 302 removed outlier: 4.735A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 307 through 315 Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.710A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.981A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N THR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N HIS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 311 removed outlier: 3.609A pdb=" N LEU A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.629A pdb=" N VAL A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.570A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.575A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 264 through 270 removed outlier: 3.678A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N HIS A 196 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU A 36 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS A 198 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU A 38 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N PHE A 200 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.522A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.233A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.857A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.747A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.505A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.468A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.598A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 1002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2230 1.34 - 1.46: 1716 1.46 - 1.58: 3146 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 7169 Sorted by residual: bond pdb=" SD FME L 1 " pdb=" CE FME L 1 " ideal model delta sigma weight residual 1.805 1.752 0.053 2.00e-02 2.50e+03 7.03e+00 bond pdb=" CG FME L 1 " pdb=" SD FME L 1 " ideal model delta sigma weight residual 1.817 1.771 0.046 2.00e-02 2.50e+03 5.40e+00 bond pdb=" N FME L 1 " pdb=" CN FME L 1 " ideal model delta sigma weight residual 1.335 1.376 -0.041 2.00e-02 2.50e+03 4.27e+00 bond pdb=" N FME L 1 " pdb=" CA FME L 1 " ideal model delta sigma weight residual 1.458 1.436 0.022 1.90e-02 2.77e+03 1.36e+00 bond pdb=" CN FME L 1 " pdb=" O1 FME L 1 " ideal model delta sigma weight residual 1.221 1.241 -0.020 2.00e-02 2.50e+03 9.64e-01 ... (remaining 7164 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.40: 154 106.40 - 113.29: 3976 113.29 - 120.18: 2450 120.18 - 127.08: 3069 127.08 - 133.97: 77 Bond angle restraints: 9726 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.72 110.98 2.74 1.30e+00 5.92e-01 4.44e+00 angle pdb=" CB MET R 197 " pdb=" CG MET R 197 " pdb=" SD MET R 197 " ideal model delta sigma weight residual 112.70 118.06 -5.36 3.00e+00 1.11e-01 3.19e+00 angle pdb=" NE ARG B 49 " pdb=" CZ ARG B 49 " pdb=" NH1 ARG B 49 " ideal model delta sigma weight residual 121.50 119.72 1.78 1.00e+00 1.00e+00 3.18e+00 angle pdb=" C ASP A 329 " pdb=" N THR A 330 " pdb=" CA THR A 330 " ideal model delta sigma weight residual 121.54 124.88 -3.34 1.91e+00 2.74e-01 3.05e+00 angle pdb=" N GLY R 232 " pdb=" CA GLY R 232 " pdb=" C GLY R 232 " ideal model delta sigma weight residual 113.18 117.16 -3.98 2.37e+00 1.78e-01 2.81e+00 ... (remaining 9721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3867 17.35 - 34.71: 300 34.71 - 52.06: 44 52.06 - 69.42: 5 69.42 - 86.77: 3 Dihedral angle restraints: 4219 sinusoidal: 1585 harmonic: 2634 Sorted by residual: dihedral pdb=" CA ASP B 254 " pdb=" CB ASP B 254 " pdb=" CG ASP B 254 " pdb=" OD1 ASP B 254 " ideal model delta sinusoidal sigma weight residual -30.00 -89.95 59.95 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CB GLU B 138 " pdb=" CG GLU B 138 " pdb=" CD GLU B 138 " pdb=" OE1 GLU B 138 " ideal model delta sinusoidal sigma weight residual 0.00 86.77 -86.77 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CG ARG B 48 " pdb=" CD ARG B 48 " pdb=" NE ARG B 48 " pdb=" CZ ARG B 48 " ideal model delta sinusoidal sigma weight residual -180.00 -137.11 -42.89 2 1.50e+01 4.44e-03 9.88e+00 ... (remaining 4216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 711 0.028 - 0.055: 261 0.055 - 0.083: 94 0.083 - 0.110: 59 0.110 - 0.138: 15 Chirality restraints: 1140 Sorted by residual: chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 1137 not shown) Planarity restraints: 1212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 148 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO R 149 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO R 149 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 149 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO B 236 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 164 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C THR B 164 " 0.024 2.00e-02 2.50e+03 pdb=" O THR B 164 " -0.009 2.00e-02 2.50e+03 pdb=" N THR B 165 " -0.008 2.00e-02 2.50e+03 ... (remaining 1209 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1848 2.81 - 3.33: 6844 3.33 - 3.85: 12019 3.85 - 4.38: 13934 4.38 - 4.90: 24486 Nonbonded interactions: 59131 Sorted by model distance: nonbonded pdb=" OD1 ASN A 270 " pdb=" OG1 THR A 325 " model vdw 2.286 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.301 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.310 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.320 2.440 nonbonded pdb=" O PRO R 286 " pdb=" OG SER R 289 " model vdw 2.328 2.440 ... (remaining 59126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.980 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.790 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 7169 Z= 0.126 Angle : 0.446 5.362 9726 Z= 0.246 Chirality : 0.039 0.138 1140 Planarity : 0.003 0.038 1212 Dihedral : 12.210 86.772 2508 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.28), residues: 898 helix: 1.85 (0.26), residues: 394 sheet: 0.37 (0.40), residues: 183 loop : -1.18 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 169 HIS 0.003 0.000 HIS B 91 PHE 0.019 0.001 PHE R 257 TYR 0.007 0.001 TYR A 231 ARG 0.006 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.704 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.9684 time to fit residues: 130.1771 Evaluate side-chains 100 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.0870 chunk 52 optimal weight: 7.9990 chunk 81 optimal weight: 0.0770 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN B 75 GLN B 230 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7169 Z= 0.160 Angle : 0.478 7.690 9726 Z= 0.254 Chirality : 0.040 0.127 1140 Planarity : 0.004 0.040 1212 Dihedral : 3.589 22.254 967 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.75 % Allowed : 12.40 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.28), residues: 898 helix: 1.77 (0.26), residues: 403 sheet: 0.09 (0.38), residues: 188 loop : -1.30 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.010 0.001 PHE R 163 TYR 0.008 0.001 TYR B 59 ARG 0.005 0.000 ARG R 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 0.781 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 116 average time/residue: 1.0577 time to fit residues: 130.3646 Evaluate side-chains 111 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 22 optimal weight: 0.0020 chunk 81 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7169 Z= 0.194 Angle : 0.481 7.474 9726 Z= 0.255 Chirality : 0.040 0.136 1140 Planarity : 0.004 0.039 1212 Dihedral : 3.776 22.392 967 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.83 % Allowed : 13.75 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 898 helix: 1.70 (0.26), residues: 402 sheet: 0.06 (0.38), residues: 188 loop : -1.24 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS C 44 PHE 0.010 0.001 PHE A 197 TYR 0.009 0.001 TYR B 59 ARG 0.004 0.000 ARG R 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.760 Fit side-chains REVERT: R 147 VAL cc_start: 0.7622 (p) cc_final: 0.7335 (m) REVERT: A 201 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7118 (t0) REVERT: A 290 GLU cc_start: 0.7360 (pm20) cc_final: 0.7115 (pm20) outliers start: 21 outliers final: 10 residues processed: 119 average time/residue: 0.9793 time to fit residues: 124.7421 Evaluate side-chains 113 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 49 optimal weight: 0.0370 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN B 259 GLN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7169 Z= 0.230 Angle : 0.512 8.061 9726 Z= 0.269 Chirality : 0.041 0.143 1140 Planarity : 0.004 0.039 1212 Dihedral : 3.988 23.430 967 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.83 % Allowed : 15.90 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.27), residues: 898 helix: 1.55 (0.25), residues: 402 sheet: 0.02 (0.37), residues: 178 loop : -1.27 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS C 44 PHE 0.012 0.001 PHE A 197 TYR 0.009 0.001 TYR B 264 ARG 0.005 0.000 ARG R 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.769 Fit side-chains REVERT: A 201 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7129 (t0) REVERT: B 78 LYS cc_start: 0.8381 (mptm) cc_final: 0.8142 (mptt) outliers start: 21 outliers final: 13 residues processed: 118 average time/residue: 0.9789 time to fit residues: 123.3545 Evaluate side-chains 116 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN C 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7169 Z= 0.192 Angle : 0.490 8.963 9726 Z= 0.255 Chirality : 0.040 0.142 1140 Planarity : 0.004 0.039 1212 Dihedral : 3.961 25.467 967 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.77 % Allowed : 17.39 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.27), residues: 898 helix: 1.61 (0.25), residues: 402 sheet: -0.06 (0.37), residues: 178 loop : -1.26 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 91 HIS 0.002 0.000 HIS C 44 PHE 0.010 0.001 PHE A 197 TYR 0.008 0.001 TYR B 124 ARG 0.005 0.000 ARG R 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 0.811 Fit side-chains outliers start: 28 outliers final: 15 residues processed: 120 average time/residue: 0.9847 time to fit residues: 126.1513 Evaluate side-chains 112 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7169 Z= 0.194 Angle : 0.495 9.439 9726 Z= 0.260 Chirality : 0.040 0.140 1140 Planarity : 0.004 0.040 1212 Dihedral : 3.997 25.840 967 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.77 % Allowed : 19.00 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.28), residues: 898 helix: 1.63 (0.26), residues: 402 sheet: -0.21 (0.36), residues: 185 loop : -1.25 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 91 HIS 0.002 0.001 HIS C 44 PHE 0.012 0.001 PHE R 161 TYR 0.009 0.001 TYR B 124 ARG 0.004 0.000 ARG R 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 0.895 Fit side-chains REVERT: A 21 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7657 (ttmm) outliers start: 28 outliers final: 18 residues processed: 117 average time/residue: 0.9795 time to fit residues: 122.6469 Evaluate side-chains 122 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 54 optimal weight: 0.0060 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 0.0040 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7169 Z= 0.153 Angle : 0.486 9.821 9726 Z= 0.253 Chirality : 0.040 0.143 1140 Planarity : 0.004 0.040 1212 Dihedral : 3.915 26.276 967 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.96 % Allowed : 19.54 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.28), residues: 898 helix: 1.74 (0.26), residues: 402 sheet: -0.15 (0.37), residues: 184 loop : -1.26 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 91 HIS 0.002 0.000 HIS B 54 PHE 0.010 0.001 PHE R 161 TYR 0.011 0.001 TYR B 124 ARG 0.006 0.000 ARG R 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 0.809 Fit side-chains REVERT: R 147 VAL cc_start: 0.7630 (OUTLIER) cc_final: 0.7332 (m) REVERT: A 17 LYS cc_start: 0.7189 (tppt) cc_final: 0.6950 (mptp) REVERT: A 21 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7656 (ttmm) REVERT: A 241 MET cc_start: 0.6926 (tpt) cc_final: 0.6360 (tpt) REVERT: A 290 GLU cc_start: 0.7424 (pm20) cc_final: 0.7189 (pm20) REVERT: B 219 ARG cc_start: 0.7601 (tpp-160) cc_final: 0.7394 (tpp-160) outliers start: 22 outliers final: 13 residues processed: 126 average time/residue: 0.9865 time to fit residues: 132.5210 Evaluate side-chains 113 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7169 Z= 0.209 Angle : 0.523 10.087 9726 Z= 0.274 Chirality : 0.041 0.143 1140 Planarity : 0.004 0.041 1212 Dihedral : 4.030 25.895 967 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.96 % Allowed : 20.62 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 898 helix: 1.65 (0.25), residues: 402 sheet: -0.17 (0.36), residues: 185 loop : -1.22 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 91 HIS 0.002 0.001 HIS C 44 PHE 0.012 0.001 PHE A 197 TYR 0.013 0.001 TYR B 124 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 0.765 Fit side-chains REVERT: A 17 LYS cc_start: 0.7199 (tppt) cc_final: 0.6951 (mptp) REVERT: A 21 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7652 (ttmm) REVERT: A 32 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7530 (ptp-170) outliers start: 22 outliers final: 15 residues processed: 116 average time/residue: 0.9505 time to fit residues: 117.9390 Evaluate side-chains 115 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 53 optimal weight: 0.0470 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7169 Z= 0.199 Angle : 0.515 10.332 9726 Z= 0.271 Chirality : 0.040 0.143 1140 Planarity : 0.004 0.041 1212 Dihedral : 4.027 26.677 967 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.56 % Allowed : 20.75 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 898 helix: 1.65 (0.25), residues: 402 sheet: -0.18 (0.36), residues: 185 loop : -1.23 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 91 HIS 0.002 0.001 HIS B 183 PHE 0.011 0.001 PHE A 197 TYR 0.012 0.001 TYR B 124 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.743 Fit side-chains REVERT: A 17 LYS cc_start: 0.7197 (tppt) cc_final: 0.6949 (mptp) REVERT: A 21 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7771 (ttmm) REVERT: A 32 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7494 (ptp-170) outliers start: 19 outliers final: 16 residues processed: 112 average time/residue: 1.0239 time to fit residues: 122.4552 Evaluate side-chains 114 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7169 Z= 0.194 Angle : 0.524 10.626 9726 Z= 0.274 Chirality : 0.040 0.143 1140 Planarity : 0.004 0.041 1212 Dihedral : 4.051 27.124 967 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.70 % Allowed : 20.75 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 898 helix: 1.65 (0.25), residues: 402 sheet: -0.12 (0.37), residues: 185 loop : -1.25 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 91 HIS 0.002 0.000 HIS C 44 PHE 0.011 0.001 PHE A 197 TYR 0.013 0.001 TYR B 124 ARG 0.005 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.815 Fit side-chains REVERT: A 17 LYS cc_start: 0.7202 (tppt) cc_final: 0.6956 (mptp) REVERT: A 21 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7757 (ttmm) REVERT: A 32 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7496 (ptp-170) outliers start: 20 outliers final: 16 residues processed: 113 average time/residue: 0.9651 time to fit residues: 116.5534 Evaluate side-chains 115 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.163278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.124615 restraints weight = 7009.092| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.79 r_work: 0.3314 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7169 Z= 0.190 Angle : 0.515 11.183 9726 Z= 0.271 Chirality : 0.040 0.144 1140 Planarity : 0.004 0.041 1212 Dihedral : 4.040 27.260 967 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.70 % Allowed : 20.75 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.28), residues: 898 helix: 1.66 (0.25), residues: 402 sheet: -0.12 (0.37), residues: 185 loop : -1.25 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 91 HIS 0.002 0.001 HIS C 44 PHE 0.011 0.001 PHE A 197 TYR 0.013 0.001 TYR B 124 ARG 0.006 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2957.37 seconds wall clock time: 53 minutes 25.07 seconds (3205.07 seconds total)